MuSeqBox

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MuSeqBox Tutorial

For a tutorial purpose, the MuSeqBox online uses a local
BLAST output file, called my_blastx_output created by
executing a BLASTX search of the entries in the query against mypept database of 28 protein sequences,
to demonstrate the usages of MuSeqBox online. We assume
that following the instruction on BLAST usage as follows,
the users may produce their own BLAST outputs and save as
local files on their machine to replace our provided
my_blastx_output

.

BLAST USAGE:

Notes: The blastx command executes a BLASTX
search of the entries in query
against mypept; the results are
saved in my_blastx_output . The "-show_gis"
option selects to display the matching peptide sequences
with the NCBI identifiers (GIs).

MUSEQBOX ONLINE USAGE:

The MuSeqBox online provides for users input file
choices. Users may use our server provided MuSeqBox
application outputs (e.g., maize EST BLASTX output, maize
contig BLASTX output, and soybean contig BLASTX output) to
search for queries of interests or supply their own BLAST
outputs. If BLAST search produces a large output file, we
strongly suggest that users download the MuSeqBox
stand-alone version to post-process the BLAST results.
Following is the tutorial showing the usage of MuSeqBox
online using a local file my_blastx_output provided by
our MuSeqBox distribution package.

Notes: By default, the MuSeqBox online uses options "-n
3" and "-p 4" to create the output (for more detailed
information, see the manual document in the distributed
package). Those options are corresponding to online
parameters Display Hits and Print format,
respectively. Users can change those parameters by
pulling down the selection menu and choose their
desirable ones. For example, to retain only the top two
BLAST hits for each query in condensed print format
(pstyle=3), users may follow the first two steps above
and do:

Note: The users may request the MuSeqBox output be sent
via their email address. To do so, the users may need to
check the checkbox left to "Send the (text format)
output to this email address:" and fill in the blank
with their email addresses.

Following steps in 1 to provide basic online settings
(i.e., Display hits and Print format) and
to select a local BLAST output file for the MuSeqBox

Clicking the checkbox left to "Select queries
based on the following criteria:"

Clicking the checkboxes left to those criteria you
wanted and fill in the blanks with the values. For
example, to select the queries with query sequence length
large than 600 and with expection value less than 1e-10,
first check both checkboxs left to QLen and
Eval, and then fill in the blanks with 600
and 1e-10, respectively

Note: This example selects those hits for which the
matching peptide sequence has HSPs covering at least 95%
of the peptide sequence, with the terminal HSPs starting
from within the first 10 amino acids of the peptide and
extending into the last 10 amino acids, respectively.
Moreover, a query sequence coverage of at least 40% is
also required. In the example, it is clear that the
maize EST AW065755 encodes the
entire homolog of the Arabidopsis 60S ribosomal protein
L18A.